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I created a small video with threshold filter to get black and white pixels (no greyscale):

ffmpeg -y -i /dev/video0
          -f lavfi -i color=0x606060:s=640x480
          -f lavfi -i color=black:s=640x480 -f lavfi
          -i color=white:s=640x480 -filter_complex threshold
          -c:v libx264 -c:a copy  test.mp4

Then I tried to convert it as a APNG file with white pixels as transparent (chromakey filter).

ffmpeg -y -i  test.mp4 -f apng -vf chromakey=white test.apng

This command converts all the pixels into transparent (checked with Gimp, it sets alpha of all pixels to 0).

Why? Also, how can I fix the command to make it work?

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I finally found how to do that in one ffmpeg command, using colorkey:

ffmpeg  -y -i /dev/video0
           -f lavfi -i color=0x6a6a6a:s=640x480
           -f lavfi -i color=black:s=640x480
           -f lavfi -i color=white:s=640x480
           -filter_complex 'threshold,colorkey=white'
           test.apng

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